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Searched refs:bsModels (Results 1 – 25 of 25) sorted by relevance

/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DAtomIteratorWithinModelSet.java35 private BS bsModels; field in AtomIteratorWithinModelSet
37 public AtomIteratorWithinModelSet(BS bsModels) { in AtomIteratorWithinModelSet() argument
38 this.bsModels = bsModels; in AtomIteratorWithinModelSet()
52 if ((modelIndex = bsModels.nextSetBit(iModel)) < 0 in set()
H A DTrajectory.java169 BS bsModels = new BS(); in getModelsSelected() local
173 bsModels.set(t); in getModelsSelected()
177 return bsModels; in getModelsSelected()
274 public void setBaseModels(BS bsModels) { in setBaseModels() argument
276 if (bsModels.get(i) && ms.am[i].isTrajectory) in setBaseModels()
277 bsModels.set(ms.am[i].trajectoryBaseIndex); in setBaseModels()
H A DModelSet.java317 if (bsModels.get(i)) in setTrajectoryBs()
673 if (bsModels.get(i)) { in includeAllRelatedFrames()
681 bsModels.set(i); in includeAllRelatedFrames()
700 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in deleteModels()
757 if (!bsModels.get(i)) { in deleteModels()
2046 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getSelectedAtomIterator()
2079 if (bsModels == null) in getModelAtomBitSetIncludingDeletedBs()
2082 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelAtomBitSetIncludingDeletedBs()
3357 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in setFrameDelayMs()
3409 if (bsModels == null || bsModels.get(i)) { in getAuxiliaryInfo()
[all …]
H A DBondCollection.java494 BS bsModels = new BS(); in assignAromaticBondsBs() local
500 bsModels.set(bond.atom1.mi); in assignAromaticBondsBs()
511 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in assignAromaticBondsBs()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DBioModelSet.java164 setAllDefaultStructure(bsModels); in calculateAllStructuresExcept()
165 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in calculateAllStructuresExcept()
203 BS bsModels = modelsOf(bsAtoms, bsModified); in getAllDefaultStructures() local
205 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in getAllDefaultStructures()
573 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) in setAllConformation()
590 BS bsModels = ms.getModelBS(bs, false); in setAllProteinType() local
591 setAllDefaultStructure(bsModels); in setAllProteinType()
995 BS bsModels = BS.newN(ms.mc); in modelsOf() local
1004 bsModels.set(modelIndex); in modelsOf()
1007 return bsModels; in modelsOf()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapespecial/
H A DEllipsoids.java53 public boolean checkObjectHovered(int x, int y, BS bsModels) { in checkObjectHovered() argument
56 Ellipsoid e = findPickedObject(x, y, false, bsModels); in checkObjectHovered()
74 BS bsModels, in checkObjectClicked() argument
79 Ellipsoid e = findPickedObject(x, y, false, bsModels); in checkObjectClicked()
108 BS bsModels) { in findPickedObject() argument
118 if (!e.visible || !bsModels.get(e.modelIndex)) in findPickedObject()
510 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
517 setVis(simpleEllipsoids, bsModels, atoms); in setModelVisibilityFlags()
518 setVis(atomEllipsoids, bsModels, atoms); in setModelVisibilityFlags()
H A DDraw.java682 BS bsModels = vwr.getVisibleFramesBitSet(); in setDrawing() local
684 if (bsModels.get(iModel) && setPoints(iModel, -1)) { in setDrawing()
1147 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
1159 if (m.modelIndex >= 0 && !bsModels.get(m.modelIndex) || m.modelFlags != null in setModelVisibilityFlags()
1160 && !BSUtil.haveCommon(bsModels, m.modelFlags)) { in setModelVisibilityFlags()
1165 m.bsMeshesVisible.and(bsModels); in setModelVisibilityFlags()
H A DDipoles.java676 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
683 dipole.visibilityFlags = ((dipole.modelIndex < 0 || bsModels in setModelVisibilityFlags()
H A DPolyhedra.java1463 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
1475 p.visibilityFlags = (p.visible && bsModels.get(p.modelIndex) in setModelVisibilityFlags()
1481 && (p.modelIndex < 0 || bsModels.get(p.modelIndex)) ? vf : 0); in setModelVisibilityFlags()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapebio/
H A DBioShapeCollection.java243 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
246 bsModels = BSUtil.copy(bsModels); in setModelVisibilityFlags()
248 ms.trajectory.setBaseModels(bsModels); in setModelVisibilityFlags()
251 b.modelVisibilityFlags = (bsModels.get(b.modelIndex) ? vf : 0); in setModelVisibilityFlags()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/
H A DAtomSetCollectionReader.java190 protected BS bsModels; field in AtomSetCollectionReader
587 bsModels = (BS) val; in initialize()
594 bsModels = (BS) htParams.get("bsModels"); in initialize()
600 if (bsModels != null || firstLastStep != null) in initialize()
602 if (bsModels == null && firstLastStep != null) { in initialize()
609 bsModels = BSUtil.newAndSetBit(firstLastStep[0]); in initialize()
612 bsModels.set(i); in initialize()
615 if (bsModels != null && (firstLastStep == null || firstLastStep[1] != -1)) in initialize()
616 lastModelNumber = bsModels.length(); in initialize()
707 boolean isOK = (bsModels == null ? desiredModelNumber < 1 in doGetModel()
[all …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/
H A DJcampdxReader.java327 BS bsModels = new BS(); in processPeakData()
341 bsModels.set(i); in processPeakData()
357 if (havePeaks && !bsModels.get(i) && id.indexOf(".") >= 0) { in processPeakData()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shape/
H A DTextShape.java238 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
241 t.visible = (t.modelIndex < 0 || bsModels.get(t.modelIndex)); in setModelVisibilityFlags()
H A DShape.java135 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
H A DMeshCollection.java636 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
646 && (mesh.modelIndex < 0 || bsModels.get(mesh.modelIndex) in setModelVisibilityFlags()
H A DMeasures.java706 BS bsModels = vwr.getVisibleFramesBitSet(); in setVisibilityInfo() local
720 if (modelIndex >= 0 && !bsModels.get(modelIndex)) in setVisibilityInfo()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/shapecgo/
H A DCGO.java260 public void setModelVisibilityFlags(BS bsModels) { in setModelVisibilityFlags() argument
264 …m.visibilityFlags = (m.isValid && m.visible && (m.modelIndex < 0 || bsModels.get(m.modelIndex)) ? … in setModelVisibilityFlags()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/viewer/
H A DPropertyManager.java999 BS bsModels = vwr.ms.getModelBS(vwr in getModelInfo() local
1015 info.put("modelsSelected", bsModels); in getModelInfo()
1019 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) { in getModelInfo()
1193 BS bsModels = vwr.ms.getModelBS(bsAtoms, true); in getModelExtract() local
1195 String title = vwr.ms.getFrameTitle(bsModels.nextSetBit(0)); in getModelExtract()
1239 ms.trajectory.selectDisplayed(bsModels); in getModelExtract()
1248 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelExtract()
1294 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels in getModelExtract()
1863 BS bsModels = vwr.ms.getModelBS(bs, true); in getPdbAtomData() local
1864 int nModels = bsModels.cardinality(); in getPdbAtomData()
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H A DViewer.java3757 public BS getModelUndeletedAtomsBitSetBs(BS bsModels) { in getModelUndeletedAtomsBitSetBs() argument
3758 return slm.excludeAtoms(ms.getModelAtomBitSetIncludingDeletedBs(bsModels), in getModelUndeletedAtomsBitSetBs()
8667 BS bsModels = (bsAtoms == null ? BSUtil.newAndSetBit(modelIndex) in deleteModels() local
8669 BS bsDeleted = ms.deleteModels(bsModels); in deleteModels()
H A DJmol.properties11068 bug fix: CIF reader with bsModels fails
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/spartan/
H A DSpartanSmolReader.java95 modelNumber = (bsModels == null && modelNo != Integer.MIN_VALUE && modelNo != 0 ? modelNo in checkLine()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/quantum/
H A DNMRCalculation.java122 BS bsModels = vwr.ms.getModelBS(bsA, false); in getInteractionTensorList() local
126 for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) { in getInteractionTensorList()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/scriptext/
H A DIsoExt.java905 BS bsModels = vwr.getVisibleFramesBitSet(); in mo() local
927 bsModels.clearAll(); in mo()
928 bsModels.set(i0); in mo()
932 for (int iModel = bsModels.nextSetBit(0); iModel >= 0; iModel = bsModels in mo()
3017 BS bsModels = vwr.ms.getModelBS(bsSelect, false); in isosurface() local
3018 if (bsModels.cardinality() > 1) in isosurface()
H A DCmdExt.java1242 BS bsModels = null; in compare() local
1245 bsModels = vwr.ms.getModelBS(bsFrom, false); in compare()
1246 bsFrames = new BS[bsModels.cardinality()]; in compare()
1247 for (int i = 0, iModel = bsModels.nextSetBit( in compare()
1248 0); iModel >= 0; iModel = bsModels.nextSetBit(iModel + 1), i++) in compare()
1251 bsModels = BSUtil.newAndSetBit(0); in compare()
1254 …for (int iFrame = 0, iModel = bsModels.nextSetBit(0); iFrame < bsFrames.length; iFrame++, iModel =… in compare()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/script/
H A DScriptEval.java4286 BS bsModels; in cmdLoad() local
4492 bsModels = (BS) getToken(i++).value; in cmdLoad()
4493 htParams.put("bsModels", bsModels); in cmdLoad()
4494 loadScript.append(" " + Escape.eBS(bsModels)); in cmdLoad()